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NCBI C++ ToolKit: src/objtools/validator/splice_problems.cpp Source File

sequence;

good_donor = ReadDonorSpliceSite(strand, stop, vec_donor, seq_len_donor, donor);

good_acceptor = ReadAcceptorSpliceSite(strand, start, vec_acceptor, seq_len_acceptor, acceptor);

donor_ok = (good_donor == eSpliceSiteRead_OK || good_donor == eSpliceSiteRead_WrongNT);

acceptor_ok = (good_acceptor == eSpliceSiteRead_OK || good_acceptor == eSpliceSiteRead_WrongNT);

(donor_ok && acceptor_ok) {

m_AcceptorProblems.push_back(

(good_acceptor, start));

m_AcceptorProblems.push_back(

(good_acceptor, start));

bad_seq =

;

(stop > 1 && stop <= seq_len) {

bad_seq = (vec[stop - 1] > 250 || vec[stop - 2] > 250);

eSpliceSiteRead_Gap;

}

(bad_seq) {

eSpliceSiteRead_BadSeq;

[0] = vec[stop - 2];

[1] = vec[stop - 1];

eSpliceSiteRead_OutOfRange;

(stop < seq_len - 2) {

bad_seq = (vec[stop + 1] > 250 || vec[stop + 2] > 250);

eSpliceSiteRead_Gap;

}

(bad_seq) {

eSpliceSiteRead_BadSeq;

[0] = vec[stop + 1];

[1] = vec[stop + 2];

eSpliceSiteRead_OutOfRange;

eSpliceSiteRead_OK;

eSpliceSiteRead_WrongNT;

eSpliceSiteRead_OK;

ReadDonorSpliceSite(strand, stop, vec, seq_len,

);

bad_seq =

;

(start < seq_len - 2) {

bad_seq = (vec[start + 1] > 250 || vec[start + 2] > 250);

eSpliceSiteRead_Gap;

}

(bad_seq) {

eSpliceSiteRead_BadSeq;

[0] = vec[start + 1];

[1] = vec[start + 2];

eSpliceSiteRead_OutOfRange;

(start > 1 && start <= seq_len) {

bad_seq = (vec[start - 2] > 250 || vec[start - 1] > 250);

eSpliceSiteRead_Gap;

}

(bad_seq) {

eSpliceSiteRead_BadSeq;

[0] = vec[start - 2];

[1] = vec[start - 1];

eSpliceSiteRead_OutOfRange;

eSpliceSiteRead_OK;

eSpliceSiteRead_WrongNT;

eSpliceSiteRead_BadSeq;

ReadAcceptorSpliceSite(strand, start, vec, seq_len,

);

has_errors =

;

(

it = m_DonorProblems.begin(); it != m_DonorProblems.end() && !has_errors; it++) {

(it->first == eSpliceSiteRead_BadSeq || it->first == eSpliceSiteRead_Gap ||

it->first == eSpliceSiteRead_WrongNT) {

(

it = m_AcceptorProblems.begin(); it != m_AcceptorProblems.end() && !has_errors; it++) {

(it->first == eSpliceSiteRead_BadSeq || it->first == eSpliceSiteRead_Gap ||

it->first == eSpliceSiteRead_WrongNT) {

m_DonorProblems.clear();

m_AcceptorProblems.clear();

m_ExceptionUnnecessary =

;

m_ErrorsNotExpected =

;

has_errors =

, ribo_slip =

;

m_ErrorsNotExpected =

;

m_ErrorsNotExpected =

;

(CSeq_loc_CI

(loc);

; ++

) {

(

.IsSetStrand()) {

strand =

.GetStrand();

}

(strand !=

) {

(!check_all && num_parts < 2) {

ValidateSpliceExon(feat, loc_handle, strand);

ValidateSpliceMrna(feat, loc_handle, strand);

ValidateSpliceCdregion(feat, loc_handle, strand);

has_errors = SpliceSitesHaveErrors();

(!m_ErrorsNotExpected && !has_errors && !ribo_slip) {

m_ExceptionUnnecessary =

;

overlap_feat_partial_5 =

;

overlap_feat_partial_3 =

;

overlap_feat_start = 0;

overlap_feat_exists =

;

overlap_feat_exists =

;

overlap_feat_exists =

;

CSeq_loc_CI

(loc);

start = range.

();

stop = range.

();

(overlap_feat_exists) {

(stop == overlap_feat_stop) {

(overlap_feat_partial_3) {

(start == overlap_feat_start) {

(overlap_feat_partial_5) {

m_AcceptorProblems.push_back(

(good_acceptor, start));

m_AcceptorProblems.push_back(

(good_acceptor, start));

m_AcceptorProblems.push_back(

(good_acceptor, start));

}

(

std::exception& ) {

ignore_mrna_partial5 =

;

ignore_mrna_partial3 =

;

ignore_mrna_partial5 =

;

ignore_mrna_partial3 =

;

CSeq_loc_CI

(loc);

CSeq_loc& part =

.GetEmbeddingSeq_loc();

start = range.

();

m_AcceptorProblems.push_back(

(good_acceptor, start));

CSeq_loc_CI tail(loc);

(; tail; ++

, ++tail) {

(bsh_head && bsh_tail) {

start = range_tail.

();

start = range_tail.

();

stop = range_head.

();

ValidateDonorAcceptorPair(

CSeq_loc& part =

.GetEmbeddingSeq_loc();

stop = range.

();

CSeq_loc_CI

(loc);

CSeq_loc& part =

.GetEmbeddingSeq_loc();

start = range.

();

m_AcceptorProblems.push_back(

(good_acceptor, start));

CSeq_loc_CI tail(loc);

(; tail; ++

, ++tail) {

(bsh_head && bsh_tail) {

start = range_tail.

();

start = range_tail.

();

stop = range_head.

();

ValidateDonorAcceptorPair(

CSeq_loc& part =

.GetEmbeddingSeq_loc();

stop = range.

();

tagSpliceSiteInfo

=

(SpliceSiteInfo) /

(

tagSpliceSiteInfo);

(

= 0;

<

; ++

) {

tagSpliceSiteInfo* entry = &SpliceSiteInfo[

];

(strand == entry->strand && entry->id == signature) {

(entry->check_donor0(donor[0]) && entry->check_donor1(donor[1]) &&

entry->check_acceptor0(acceptor[0]) && entry->check_acceptor1(acceptor[1]));

tagSpliceSiteInfo

=

(SpliceSiteInfo) /

(

tagSpliceSiteInfo);

(

= 0;

<

; ++

) {

tagSpliceSiteInfo* entry = &SpliceSiteInfo[

];

(strand == entry->strand && entry->id == signature) {

(entry->check_site0(

[0]) && entry->check_site1(

[1]));

@ eExtreme_Biological

5' and 3'

ESubtype GetSubtype(void) const

SeqVector related exceptions.

namespace ncbi::objects::

bool SpliceSitesHaveErrors()

void ValidateSpliceCdregion(const CSeq_feat &feat, const CBioseq_Handle &bsh, ENa_strand strand)

void CalculateSpliceProblems(const CSeq_feat &feat, bool check_all, bool pseudo, CBioseq_Handle loc_handle)

void ValidateSpliceExon(const CSeq_feat &feat, const CBioseq_Handle &bsh, ENa_strand strand)

ESpliceSiteRead ReadAcceptorSpliceSite(ENa_strand strand, TSeqPos start, const CSeqVector &vec, TSeqPos seq_len, TSpliceSite &site)

ESpliceSiteRead ReadDonorSpliceSite(ENa_strand strand, TSeqPos stop, const CSeqVector &vec, TSeqPos seq_len, TSpliceSite &site)

void ValidateSpliceMrna(const CSeq_feat &feat, const CBioseq_Handle &bsh, ENa_strand strand)

pair< size_t, TSeqPos > TSpliceProblem

void ValidateDonorAcceptorPair(ENa_strand strand, TSeqPos stop, const CSeqVector &vec_donor, TSeqPos seq_len_donor, TSeqPos start, const CSeqVector &vec_acceptor, TSeqPos seq_len_acceptor)

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static const char si[8][64]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ eOverlap_Contains

2nd contains 1st extremes

@ eOverlap_Contained

2nd contained within 1st extremes

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

ENa_strand

strand of nucleic acid

const struct ncbi::grid::netcache::search::fields::SIZE size

bool CheckIntronAcceptor(ENa_strand strand, TConstSpliceSite acceptor)

static const char * kSpliceSiteGT

bool CheckIntronSpliceSites(ENa_strand strand, TConstSpliceSite donor, TConstSpliceSite acceptor)

static bool s_EqualsA(Char c)

static const char * kSpliceSiteGTAG

static const char * kSpliceSiteATAC

static const char * kSpliceSiteGCAG

static const char * kSpliceSiteAG

static const char * kSpliceSiteGC

static bool s_EqualsT(Char c)

static bool s_EqualsG(Char c)

bool CheckAdjacentSpliceSites(const string &signature, ENa_strand strand, TConstSpliceSite donor, TConstSpliceSite acceptor)

static bool s_EqualsC(Char c)

bool CheckIntronDonor(ENa_strand strand, TConstSpliceSite donor)

bool CheckSpliceSite(const string &signature, ENa_strand strand, TConstSpliceSite site)

Char const (& TConstSpliceSite)[2]

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